6-157968709-C-T

Variant names:

• chr6-157968709-C-T
• rs9458975

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.418 in 142,488 control chromosomes in the GnomAD database, including 12,128 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.42 (12128 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.418 AC: 59497 AN: 142416 Hom.: 12117 Cov.: 26

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.402

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.418 AC: 59525 AN: 142488 Hom.: 12128 Cov.: 26 AF XY: 0.408 AC XY: 28317 AN XY: 69328

African (AFR) AF: 0.482 AC: 16766 AN: 34804

American (AMR) AF: 0.333 AC: 4867 AN: 14624

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1256 AN: 3446

East Asian (EAS) AF: 0.306 AC: 1536 AN: 5024

South Asian (SAS) AF: 0.320 AC: 1498 AN: 4680

European-Finnish (FIN) AF: 0.286 AC: 2759 AN: 9654

Middle Eastern (MID) AF: 0.356 AC: 99 AN: 278

European-Non Finnish (NFE) AF: 0.441 AC: 29611 AN: 67102

Other (OTH) AF: 0.398 AC: 788 AN: 1980

Alfa AF: 0.438 Hom.: 32050

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.48
DANN	Benign	0.53
PhyloP100		-0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9458975; hg19: chr6-158389741;